Contacts of the helix formed by residues 72 - 89 (chain C) in PDB entry 1RZR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASN 72 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69C ASP* 3.0 20.2 + - + +
71C SER* 1.3 77.4 - - - +
73C ILE* 1.3 75.1 + - - +
74C PHE* 2.7 43.4 + - - +
75C TYR* 3.1 24.5 + - + -
76C ALA* 3.2 9.9 + - - -
249C GLU* 5.4 5.5 + - - -
278G ARG* 4.7 20.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 73 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71C SER 3.6 5.7 + - - +
72C ASN* 1.3 77.2 - - - +
74C PHE* 1.3 87.4 + - + +
76C ALA* 3.8 7.2 - - - +
77C GLU* 3.0 29.5 + - - +
275C ASP* 5.9 0.4 - - - +
277C THR* 3.6 38.6 - - + +
278C ARG* 3.8 29.4 - - - +
279C LEU* 5.4 7.9 - - + -
71G SER 4.6 9.0 - - - +
73G ILE* 4.9 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72C ASN* 2.7 23.8 + - - +
73C ILE* 1.3 89.1 - - + +
75C TYR* 1.3 78.9 + + + +
77C GLU* 3.3 6.6 + - - +
78C LEU* 3.1 24.5 + - + +
146C ALA* 5.5 5.8 - - + -
161C TYR* 5.2 2.0 - + - -
275C ASP* 3.7 15.9 - - - +
292C GLN* 3.5 31.4 - - - -
294C MSE 3.0 41.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 75 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67C ILE* 4.0 17.8 - - + +
68C PRO* 3.2 49.2 - - + +
69C ASP* 3.2 36.8 - - + +
70C ILE* 5.0 0.2 - - - -
72C ASN* 3.1 16.4 + - + -
74C PHE* 1.3 95.5 - + + +
76C ALA* 1.3 52.2 + - - +
78C LEU* 2.8 21.7 + - + +
79C ALA* 2.4 40.3 + - - +
100C GLN* 3.5 11.6 + - - +
123C MSE 4.7 4.3 - - + -
124C SER 5.7 1.0 - - - -
125C GLY* 5.4 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 76 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70C ILE* 3.5 25.4 + - + +
72C ASN 3.2 7.8 + - - +
73C ILE* 3.8 10.5 - - - +
75C TYR* 1.3 77.2 - - - +
77C GLU* 1.3 53.5 + - - +
79C ALA* 3.2 9.0 + - - +
80C ARG* 2.7 34.1 + - - +
70G ILE* 3.3 26.8 - - - +
71G SER* 4.1 8.1 - - - +
76G ALA* 4.1 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 77 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ILE* 3.0 27.3 + - - +
74C PHE 3.7 3.1 - - - +
76C ALA* 1.3 72.7 - - - +
78C LEU* 1.3 56.7 + - - +
80C ARG* 3.1 8.5 + - + +
81C GLY* 2.7 30.7 + - - -
277C THR* 4.3 12.5 - - - +
278C ARG* 4.1 27.3 + - - +
294C MSE 3.8 33.4 - - + +
295C TYR* 4.1 16.2 - - + +
71G SER* 3.4 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74C PHE* 3.1 17.2 + - + +
75C TYR* 2.8 23.1 + - + +
77C GLU* 1.3 76.5 - - - +
79C ALA* 1.3 61.1 + - - +
81C GLY* 2.9 12.3 + - - -
82C ILE* 3.0 11.4 + - - +
123C MSE 3.6 32.1 - - + -
145C ALA* 4.5 5.6 - - + +
146C ALA* 4.2 22.2 - - + -
294C MSE 3.0 36.7 + - + +
297C ILE* 3.8 8.7 - - + -
298C GLY* 3.0 31.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 79 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 6.0 0.4 - - + -
67C ILE* 5.0 7.1 - - + +
70C ILE* 3.9 22.7 - - + -
75C TYR 2.4 29.8 + - - +
76C ALA 3.4 5.2 - - - +
78C LEU* 1.3 65.3 - - - +
80C ARG* 1.3 67.1 + - - +
82C ILE* 2.9 22.8 + - - +
83C GLU* 3.0 15.2 + - - +
93C ILE* 5.5 2.1 - - - +
95C LEU* 4.9 10.5 - - + -
70G ILE* 3.8 14.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 80 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ALA 2.7 17.2 + - - +
77C GLU* 3.3 8.5 - - + +
79C ALA* 1.3 73.1 - - - +
81C GLY* 1.3 67.0 + - - +
82C ILE 3.0 0.3 + - - -
83C GLU* 3.1 0.9 + - - -
84C ASP* 2.7 58.4 + - - +
295C TYR* 4.1 11.0 - - + -
68G PRO 4.0 1.2 + - - -
69G ASP* 2.3 48.7 + - - +
70G ILE* 3.5 8.0 - - + +
71G SER* 3.7 15.0 - - - -
97G ASN* 3.5 33.3 + - - +
99G ASP* 3.2 31.3 + - - -
104G LYS* 5.2 1.6 - - - +
17T ARG* 3.0 27.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 81 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU 2.7 14.0 + - - -
78C LEU 2.9 6.5 + - - -
80C ARG* 1.3 78.2 - - - +
82C ILE* 1.3 59.7 + - - +
84C ASP* 4.0 1.7 + - - +
85C ILE* 3.4 13.2 + - - +
295C TYR* 3.6 33.9 - - - -
299C ALA* 3.2 22.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 82 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65C VAL* 4.3 15.0 - - + -
78C LEU 3.0 11.5 + - - +
79C ALA* 2.9 13.6 + - - +
81C GLY* 1.3 74.6 - - - +
83C GLU* 1.3 58.7 + - - +
85C ILE* 3.1 6.8 + - - +
86C ALA 2.8 30.1 + - - -
93C ILE* 4.6 13.7 - - + -
121C ILE* 3.7 18.8 - - + -
123C MSE 3.1 36.3 - - + -
298C GLY* 3.5 26.2 - - - +
302C MSE 3.0 34.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ALA 3.0 13.8 + - - +
80C ARG 3.7 1.6 - - - +
82C ILE* 1.3 79.3 - - - +
84C ASP* 1.3 69.8 + - - +
86C ALA* 3.1 6.1 + - - +
87C THR* 2.8 36.8 + - - -
91C TYR 4.6 5.5 - - - +
92C ASN* 5.6 0.7 - - - -
93C ILE* 4.0 18.8 + - + +
846C SO4 4.8 0.3 + - - -
70G ILE* 4.6 3.1 - - + -
95G LEU* 3.7 20.9 - - + +
96G SER* 3.2 30.8 + - - -
97G ASN* 3.1 35.0 + - - +
104G LYS* 5.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 84 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C ARG* 2.7 50.4 + - - +
81C GLY 4.3 1.6 - - - +
83C GLU* 1.3 84.6 - - - +
85C ILE* 1.3 62.7 + - + +
87C THR* 3.7 8.0 - - - +
88C MSE 2.9 26.5 + - - +
295C TYR* 2.9 35.8 + - - +
97G ASN* 4.6 0.5 - - - +
104G LYS* 5.4 3.3 + - - -
17T ARG* 3.7 8.7 - - - +
20T THR* 4.8 5.6 - - - +
24T GLN* 4.4 6.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 85 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81C GLY 3.4 15.9 - - - +
82C ILE 3.1 8.1 + - - +
84C ASP* 1.3 77.3 - - - +
86C ALA* 1.3 66.2 + - - +
87C THR 3.1 1.3 - - - -
88C MSE 3.0 22.5 + - + +
89C TYR* 2.9 38.2 + - + -
299C ALA* 3.6 27.1 - - + +
302C MSE 3.4 18.6 - - + -
303C ARG* 3.9 12.1 - - + +
20T THR* 3.8 27.1 - - + -
47T ILE* 4.1 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 86 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82C ILE 2.8 17.7 + - - +
83C GLU* 3.8 3.6 - - - +
85C ILE* 1.3 70.6 - - - +
87C THR* 1.3 60.0 + - - +
89C TYR* 3.0 10.8 + - - -
90C LYS 3.0 0.3 + - - -
91C TYR* 2.7 47.8 + - + +
93C ILE* 3.5 31.9 - - + -
302C MSE 3.5 19.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C GLU* 2.8 30.0 + - - -
84C ASP* 3.7 7.2 - - - +
86C ALA* 1.3 73.3 - - - +
88C MSE 1.3 60.6 + - - +
89C TYR 2.9 4.7 - - - -
90C LYS* 2.7 28.4 + - - +
91C TYR 3.7 7.0 + - - -
846C SO4 2.5 31.0 + - - +
96G SER* 3.9 4.0 + - - -
104G LYS* 4.9 17.3 + - - +
24T GLN* 5.5 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MSE 88 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASP 2.9 17.5 + - - +
85C ILE* 3.0 19.7 + - - +
87C THR* 1.3 78.4 - - - +
89C TYR* 1.3 89.1 + - + +
90C LYS* 3.8 2.9 + - - +
20T THR 5.2 0.2 - - - +
23T VAL* 4.4 2.7 - - + -
24T GLN* 3.2 41.7 - - + +
27T SER* 4.2 22.9 - - - +
45T LYS 4.8 2.5 - - - +
47T ILE* 3.8 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 89 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 2.9 29.2 + - + +
86C ALA* 3.1 5.6 - - - +
87C THR 2.9 1.0 - - - -
88C MSE 1.3 111.6 - - + +
90C LYS* 1.3 67.4 + - - +
91C TYR* 3.1 18.0 - - + -
303C ARG* 2.8 48.2 + - - -
306C THR* 3.5 29.4 - - + -
45T LYS 4.7 7.4 + - - -
47T ILE* 4.8 4.1 + - + +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il